My understanding, and I could be wrong, is that 100% of reviews involve the on-field official going under the hood. The difference in this case is that scoring plays or turnovers are "automatically" reviewed by the league office. If they deem there's something "worth looking at", they flag the on-field official and he goes under the hood.
So on the INT that involved would looked to me to be pass interference, the league office looked at the play and didn't feel it warranted calling the on-field ref to review it.
On the second INT, which looked to me like the ground aided the catch, that one WAS flagged by the league office, and the ref went under the hood to review. No challenge flag... that's an automatic review.
On the catch/fumble out of bounds, that was challenged by Harbaugh I believe, so that's a under the hood review.
I'm pretty sure this is correct, because I don't recall an instance where the NY review team overturned a call on the field without the head official being in the booth to review. The NY teams job is to flag turnover/scoring plays for review, if it warrants a review, and then assist the on-field ref with the videos and rule discussions.
My problem with the first non-call for the PI was that the league office didn't even feel like it was worth it for the on-field ref to take a look. I think that's a mistake.